rs4240803
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003486.7(SLC7A5):c.539-3748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,718 control chromosomes in the GnomAD database, including 9,538 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.34 ( 9538 hom., cov: 32)
Consequence
SLC7A5
NM_003486.7 intron
NM_003486.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.00
Genes affected
SLC7A5 (HGNC:11063): (solute carrier family 7 member 5) Enables L-leucine transmembrane transporter activity; L-tryptophan transmembrane transporter activity; and thyroid hormone transmembrane transporter activity. Involved in carboxylic acid transport; thyroid hormone transport; and xenobiotic transport. Located in cytosol; intracellular membrane-bounded organelle; and plasma membrane. Is integral component of membrane. Part of amino acid transport complex; apical plasma membrane; and microvillus membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC7A5 | NM_003486.7 | c.539-3748C>T | intron_variant | ENST00000261622.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC7A5 | ENST00000261622.5 | c.539-3748C>T | intron_variant | 1 | NM_003486.7 | P1 | |||
SLC7A5 | ENST00000565644.5 | c.-260-3748C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.340 AC: 51611AN: 151600Hom.: 9521 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.341 AC: 51661AN: 151718Hom.: 9538 Cov.: 32 AF XY: 0.353 AC XY: 26138AN XY: 74096
GnomAD4 genome
?
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AC:
51661
AN:
151718
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32
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26138
AN XY:
74096
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Asia WGS
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1845
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at